June 2007 - users-list

[MonetDB-users] newbie question, Debian install, can't connect
by Matt Stucky 12 Jun '07

12 Jun '07

downloaded the super tarball, installed from the top-level shell script, all seemed ok. mserver5 starts, io.print("test"); works as expected. but when I try to connect with mjclient i get: matt@debian5150:/root/MonetDB/bin$ ./mjclient -umonetdb -lsql password: Database connect failed: MALException:setScenario:Scenario 'sql' not initialized what am i doing wrong? thanks for the help in advance. matt ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The Preacher Said: "Oh Lord, without you we are but dust!" And the Child Said: "What's butt dust?" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AOL & Yahoo IM: stuckym44 MSN Messenger: stuckym4 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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[MonetDB-users] Fwd: MonetDB Error
by Venks 08 Jun '07

08 Jun '07

Niels/Fabian/Romulo, Thanks for all your replies. I rebooted the server and was able to bring up the database again. Next time, if this happens I will try to remove the locks. I tried to remove the file ".gdk_lock" but Linux wouldn't allow me to remove it. Meanwhile, let me do more tests and see why this is becoming an issue. If necessary as Niels suggested I will open a bug as the query actually crashed the server instead of just returning an error. Niels, Though I am joining all these tables, I have WHERE conditions on each table and the end result is actually 16,384 rows. I will do some more testing by changing the syntax of the query and see if it helps. Forwarded Conversation Subject: MonetDB Error ------------------------ From: Venks <venkatesh.mantha(a)gmail.com> To: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:12 AM I got the following error while trying to run a query joining 10 tables. These tables are all 2 or 3 column tables but do have on an average 10M rows in each table. =================== lin5 kernel: journal_get_undo_access: No memory for committed data mserver5: /scratch/monet.GNU.64.64.d.5883/MonetDB5/src/optimizer/opt_joinpath.mx:227: ALGjoinPath: Assertion `b' failed. ./startmonet.sh: line 2: 9488 Aborted $MONETDB5_PREFIX/bin/mserver5 --dbname=csdb --dbinit='include sql;' ====================== After the above error, I am unable to start the MonetDB database. I get the following error. !FATAL: GDKlockHome: Database lock '.gdk_lock' denied How can I re-start the server? Thanks, - Venks -------- From: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:19 AM [Quoted text hidden]You need to remove your dbfarm and dblogs. Just do rm -fr $MONETDB5_PREFIX/var/* Regards, Romulo > > > How can I re-start the server? > > Thanks, > > - Venks > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > MonetDB-users mailing list > MonetDB-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-users -------- From: Venks <venkatesh.mantha(a)gmail.com> To: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:27 AM If I remove /var/* that will wipe-out my entire database. Correct? [Quoted text hidden] -------- From: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:30 AM Venks wrote: > If I remove /var/* that will wipe-out my entire database. Correct? Yes. Regards, Romulo [Quoted text hidden] -------- From: Venks <venkatesh.mantha(a)gmail.com> To: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:31 AM Is there any way I can restart MonetDB without loosing all my data? [Quoted text hidden] -------- From: Niels Nes <Niels.Nes(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Date: Fri, Jun 8, 2007 at 9:34 AM On Fri, Jun 08, 2007 at 09:12:50AM -0400, Venks wrote: > I got the following error while trying to run a query joining 10 > tables. These tables are all 2 or 3 column tables but do have on an > average 10M rows in each table. > > =================== > > lin5 kernel: journal_get_undo_access: No memory for committed data This kernel message seems to indicate that monet run out of memory. 10M^10 is really big, so unless you had a very selective join condition this will blow up to extreme big tables. > mserver5: /scratch/monet.GNU.64.64.d.5883/MonetDB5/src/optimizer/opt_joinpath.mx:227: > ALGjoinPath: Assertion `b' failed. > ./startmonet.sh: line 2: 9488 Aborted Afcourse a crash shouldn't happen. > $MONETDB5_PREFIX/bin/mserver5 --dbname=csdb --dbinit='include sql;' > > ====================== > > After the above error, I am unable to start the MonetDB database. I > get the following error. and after restarting it should normally work even with a crash. So these are bugs, could you report them. Together with a script or so which triggers it? Many thanks.. Niels > > > !FATAL: GDKlockHome: Database lock '.gdk_lock' denied > > > How can I re-start the server? > > Thanks, > > - Venks > [Quoted text hidden]-- Niels Nes, Centre for Mathematics and Computer Science (CWI) Kruislaan 413, 1098 SJ Amsterdam, The Netherlands room C0.02, phone ++31 20 592-4098, fax ++31 20 592-4312 url: http://www.cwi.nl/~niels e-mail: Niels.Nes(a)cwi.nl -------- From: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:35 AM Venks wrote: > Is there any way I can restart MonetDB without loosing all my data? Of course. Just kill your server and start it again.. [goncalve@amelia Triggers]$ ps aux | grep mserver goncalve 27450 1.8 4.8 338904 99192 pts/0 Sl+ 15:34 0:00 mserver5 goncalve 27484 0.0 0.0 60240 708 pts/2 R+ 15:34 0:00 grep mserver [goncalve@amelia Triggers]$ kill -9 27450 [goncalve@amelia Triggers]$ ps aux | grep mserver goncalve 27491 0.0 0.0 60244 708 pts/2 S+ 15:34 0:00 grep mserver [goncalve@amelia Triggers]$ [Quoted text hidden] -------- From: Fabian Groffen <Fabian.Groffen(a)cwi.nl> Reply-To: monetdb-users(a)lists.sourceforge.net, monetdb-users(a)lists.sourceforge.net To: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:36 AM On 08-06-2007 09:31:45 -0400, Venks wrote: > Is there any way I can restart MonetDB without loosing all my data? Make sure there are no running mservers any more. If there still are, kill 'em all. Find the .gdk_lock file in your var/monetdb/... and remove it. Try to start MonetDB. (Preferably without the script so you can see what happens.) If it fails to load the BATs, the database has been corrupted. [Quoted text hidden] -------- From: Niels Nes <Niels.Nes(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Date: Fri, Jun 8, 2007 at 9:36 AM On Fri, Jun 08, 2007 at 09:31:45AM -0400, Venks wrote: > Is there any way I can restart MonetDB without loosing all my data? > > > >> > > > >> > After the above error, I am unable to start the MonetDB database. I > > >> > get the following error. > > >> > > > >> > > > >> > !FATAL: GDKlockHome: Database lock '.gdk_lock' denied If the lock is the only problem you could simply remove this, ie do a find $prefix/var/ -name .gdk_lock | xargs rm -f This will remove all gdk_lock files, so be sure there are no running Mserver/mserver5s. niels > > >> You need to remove your dbfarm and dblogs. > > >> > > >> Just do > > >> rm -fr $MONETDB5_PREFIX/var/* > > >> > > >> Regards, > > >> Romulo > > >> > > > >> > > > >> > How can I re-start the server? > > >> > > > >> > Thanks, > > >> > > > >> > - Venks > > >> > > > >> > > > >> ------------------------------------------------------------------------- > > >> > This SF.net email is sponsored by DB2 Express > > >> > Download DB2 Express C - the FREE version of DB2 express and take > > >> > control of your XML. No limits. Just data. Click to get it now. > > >> > http://sourceforge.net/powerbar/db2/ > > >> > _______________________________________________ > > >> > MonetDB-users mailing list > > >> > MonetDB-users(a)lists.sourceforge.net > > >> > https://lists.sourceforge.net/lists/listinfo/monetdb-users > > >> > > >> > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > MonetDB-users mailing list > MonetDB-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-users [Quoted text hidden] --------

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[MonetDB-users] MonetDB Error
by Venks 08 Jun '07

08 Jun '07

I got the following error while trying to run a query joining 10 tables. These tables are all 2 or 3 column tables but do have on an average 10M rows in each table. =================== lin5 kernel: journal_get_undo_access: No memory for committed data mserver5: /scratch/monet.GNU.64.64.d.5883/MonetDB5/src/optimizer/opt_joinpath.mx:227: ALGjoinPath: Assertion `b' failed. ./startmonet.sh: line 2: 9488 Aborted $MONETDB5_PREFIX/bin/mserver5 --dbname=csdb --dbinit='include sql;' ====================== After the above error, I am unable to start the MonetDB database. I get the following error. !FATAL: GDKlockHome: Database lock '.gdk_lock' denied How can I re-start the server? Thanks, - Venks

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[MonetDB-users] Error during making buildtools (branch MonetDB_1-18)
by Ying Zhang 06 Jun '07

06 Jun '07

Hi all, I have just checked out the release branch and try to rebuild everything from scratch (on andorea). Making buildtools gives the following error: Making install in conf make[1]: Entering directory `/export/scratch1/zhang/monet/stable/buildtools/build-debug/conf' make[1]: *** No rule to make target `buildtools-config', needed by `all-am'. Stop. make[1]: Leaving directory `/export/scratch1/zhang/monet/stable/buildtools/build-debug/conf' make: *** [install-recursive] Error 1 Does anyone have an idea about this? I believe that building environment is clean. Thanks! Jennie

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[MonetDB-users] building monetdb5 on windows
by Colin Foss 05 Jun '07

05 Jun '07

Are there any plans to create a script similar to monetdb-install.sh for Windows?

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[MonetDB-users] XRPC problem: too many parameters
by Makoto YUI 02 Jun '07

02 Jun '07

Hi, I caught an error (see attached file) at the remote method invocation of XRPC. While I'm not sure whether my query is correct or not, is there imitation of parameters in XRPC? The query and dataset used in the evaluation are put on here. http://db-www.naist.jp/~makoto-y/tmp/xrpc.tgz Thanks, Makoto YUI P.S. To: list-admin please ignore previous mail from wrong address MAPI = monetdb@localhost:50000 QUERY = import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit ERROR = !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. MAPI = monetdb@localhost:50000 QUERY = import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit ERROR = !ERROR: doLoopLiftedRPC: execution failed at all destinations mapi_query_part:1705:import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit where $hit/Hit_num = 1 and $hit/Hit_hsps/Hsp/Hsp_evalue/text() <= 1.0e-8 return $e), $uniprot_entry := (for $e in $blast-uniprot/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit where $hit/Hit_num = 1 and $hit/Hit_hsps/Hsp/Hsp_evalue/text() <= 1.0e-8 return $e) where $gb_entry/BlastOutput_query-def/text() = $uniprot_entry/BlastOutput_query-def/text() return <result> { let $gb-hit := $gb_entry/BlastOutput_iterations/Iteration/Iteration_hits/Hit, $gb-key := $gb-hit/Hit_gb/text() return let $genbank-remote-entries := execute at {$remote-endpoint} { test:q1($gb-key) } for $remote_entry at $pos in $genbank-remote-entries let $gb_definition := $remote_entry/INSDSeq_definition, $gb_feature := $remote_entry/INSDSeq_feature-table/INSDFeature, $blast_evalue := $gb-hit[Hit_gb/text() = $remote_entry/INSDSeq_accession-version/text()]/Hit_hsps/Hsp/Hsp_evalue return <genbank num="{ $pos }">{ $blast_evalue, $gb_definition, $gb_feature } </genbank> } </result> fetch next block: start at:2 got next block: length:269 text:XRPC_Client_Serialisation: 626 microsec !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations got complete block: text:XRPC_Client_Serialisation: 626 microsec !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:XRPC_Client_Serialisation: 626 microsec allocating new result set XRPC_Client_Serialisation: 626 microsec got complete block: text:!WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" allocating new result set got complete block: text:!ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: CMDhttp_post: too many parameters. got complete block: text:!ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: CMDhttp_post: operation failed. got complete block: text: !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line: closing result set got complete block: text:!ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: doLoopLiftedRPC: execution failed at all destinations allocating new result set fetch next block: start at:271 got next block: length:0 text: got complete block: text: read_line: closing result set closing result set Timer 1014.527 msec

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[MonetDB-users] Data Load Issue
by Venks 01 Jun '07

01 Jun '07

Hi, I am trying to load a 12.8 Million row table using COPY command. The table has about 256 columns. After 4 or 5 hours of running, the server terminated abruptly. I am running this on a AMD 64 Bit running Redhat Linux with 3GB of memory and lots of swap space. Any help in identifying the issue would be appreciated. Thanks, - Venks

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